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Data and Analysis for Kaplanis, Denny, and Raimondi 2024, "Vertical distribution of rocky intertidal organisms shifts with sea-level variability on the Northeast Pacific Coast".
<p>This repository contains all the data and R scripts used to produce all analyses and figures for Kaplanis, Denny, and Raimondi 2024, as well as all intermediate outputs and final figures. To access this content, download and unzip the intertidalvertdist folder (for intertidal vertical distribution). The R Project is titled "intertidalvertdist". All pertinent information needed to access data, replicate the analyses, and produce figures is contained within the README file, but a brief desciption is below.</p> <p><br>Directory Architecture:</p> <p>Data:<br>Contains all data. Within this folder are two subdirectories - Raw Data, and Processed Data. Raw Data are unmanipulated, straight from the data source. Processed Data are outputs from scripted data wrangling and transformations. </p> <p>Within each of these folders are two more subdirectories: Tide Gauge Data, and MARINe Data. These are the two data sources used in this manuscript - monthly sea-level data from The National Oceanic and Atmospheric Administration Center for Operational Oceanographic Products and Services (NOAA CO-OPS) tide gauge stations, and long-term rocky intertidal biological monitoring data from Multi-Agency Rocky Intertidal Network (MARINe) survey sites.</p> <p>Scripts:<br>All R scripts are contained within the Scripts folder. The scripts have the prefix IVD (for intertidal vertical distribution), then a name that indicates the major function of the code. The scripts either downloads data, manipulates data, conducts analyses, and/or produces a figure.</p> <p>Outputs:<br>Any figures and tables from preliminary analyses, but that are not used in the final manuscript, are saved in Outputs.</p> <p>Figures:<br>All final figures and tables are contained in the Figures folder. All figures are produced by scripts, except Figs. 1 and 2, which are schematics produced manually in a graphics editor. This folder contains two other folders: Supplemenatary Figures, and Partial Regression Plots. Partial Regression plots are the same as the final Figures 8-12, except they are grouped by taxa rather than by explanatory variable.</p> <p>Data Processing Workflow - Overview: <br>Tide Gauge Data (Data/Raw Data/Tide Gauge Data/individual stations) were downloaded using the NOAA Co-Ops API URL Builder (https://tidesandcurrents.noaa.gov/api-helper/url-generator.html), merged, then analyzed. Three MARINe data sets from the Coastal Biodiversity Survey (CBS) were accessed via data requests (https://marine.ucsc.edu/explore-the-data/contact/data-request-form.html). The first MARINe dataset (Data/Raw Data/MARINe Data/CBS_Percent Cover Data, both First Sample and Full Sample) was used to determine the top ten most abundant taxa (hereafter termed “dominant taxa”) across CBS survey sites during the monitoring period of 2001-01-01 to 2021-09-30. The second MARINe dataset (Data/Raw Data/MARINe Data/CBS_Elevation Data) was used to describe the upper limits of vertical distribution of dominant taxa through time. The third MARINe dataset (Data/Raw Data/MARINe Data/CBS_Presence Data) was used to visualize latitudinal distribution of taxa.</p> <p>Location information for Tide Gauge Stations and CBS Survey Sites were assembled into a table (Data/Raw Data/CBS_Tide Gauge_Data.csv)</p> <p>Tide Gauge Data were processed first, then MARINe Data. To replicate this workflow follow the steps described in the README file, in order.</p>
Biodiversity and metacommunity structure of rocky intertidal invertebrates in some coastal ecosystems in Puerto Rico
The goals of this study were to determine the relative importance of environmental (wave power density, wave height) and habitat (e.g., algal cover, slope, complexity of rock surfaces) factors associated with the structure of local assemblages at multiple shore heights and the regional metacommunity of mobile invertebrates on oceanic rocky intertidal habitats. These characteristics and abundances of 41 species of invertebrate were estimated at 10 plots at each of three tidal heights at each of ten sites on the shoreline of Puerto Rico. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Figure 31 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 31. Bryopesanser latesco Tilbrook: (a) NSMT-Te 1167, autozooids; (b) NSMT-Te 1100, orifice; (c) NSMT-Te 1054, ovicelled and non-ovicelled autozooids; (d) NSMT-Te 1103, ovicelled and nonovicelled autozooids; note sharp projection on proximal peristomial rim in lower-right zooid, and size difference in avicularia between lower right and lower left zooids. Panels are scanning electron microscopic images of dried, unbleached specimen (a) or bleached specimens (b–d). Scale bars: a, c, d = 300 µm; b = 100 µm.
Figure 37 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 37. Rhynchozoon lunifrons sp. nov.: (a) NSMT-Te 1196 (paratype), colony view; (b) enlargement from preceding panel, showing autozooids typically having three processes associated with orifice; (c–f) NSMT-Te 1197 (paratype), (c) marginal autozooids showing shape and orientation of suboral avicularian chamber, (d) marginal autozooids, showing orifice shape, (e) well-calcified ovicelled autozooids, showing large semicircular area of exposed entooecium on ovicell, (f) endozooidal ovicells, with three zooids showing a second ovicell (arrowheads) lateral to orifice. All panels are scanning electron microscopic images of bleached specimens. Scale bars: a = 1.0 mm; b = 500 µm; c–f = 300 µm.
Figure 29 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 29. Arthropoma harmelini sp. nov., NSMT-Te 1159 (holotype): (a) autozooids, showing crescentic suboral umbo, which in top-centre zooid is continuous with peristomial rim; (b) orifice; (c) ovicelled autozooids, with one ovicell showing a lateral extension; note there is no row of pseudopores between orifice and floor of developing ooecium; (d) ovicelled and non-ovicelled autozooids; (e) autozooids with developing ooecia; note lack of pseudopores between orifice and floor of ooecium; (f) colony margin, showing interzooidal connections. All panels are scanning electron microscopic images of bleached specimen. Scale bars: a, c, e, f = 300 µm; b = 100 µm; d = 500 µm.
Figure 34 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 34. Rhynchozoon ferocula Hayward: (a) NSMT-Te 1178, view of smaller colony on SEM stub; (b) NSMT-Te 1179, marginal autozooids; (c–e) NSMT-Te 1178 (larger colony on SEM stub), (c) orifices in (c) mature autozooids, (d) orifice and oral spines, (e) ovicelled autozooids (arrowhead, window in calcified ectooecium; arrow, labellum); (f) NSMT-Te 1180, ancestrula and two daughter zooids. All panels are scanning electron microscopic images of bleached specimens. Scale bars: a = 1.0 mm; b, e, f = 200 µm; c = 100 µm; d = 50 µm.
Figure 32 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 32. (a, b) Crepidacantha longiseta Canu and Bassler: (a) NSMT-Te 1167, autozooids; (b) NSMT- Te 1169, ovicelled and non-ovicelled autozooids. (c, d) Crepidacantha poissonii (Audouin), NSMT-Te 1100: (c) ovicelled autozooids; (d) ovicelled and non-ovicelled autozooids. Panels are scanning electron microscopic images of dried, unbleached (a, c) or bleached (b, d) specimens. Scale bars: a, c = 300 µm; b, d = 200 µm.
Figure 39 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 39. Rhynchozoon ryukyuense sp. nov., NSMT-Te 1202 (a–c), NHMUK 2016.5.13.81 (d, e), NSMT- Te 1201 (f), all paratype specimens: (a) colony view; (b) marginal autozooids, showing aspect of suboral avicularian chamber; (c) marginal autozooids, showing shape and orientation of avicularian rostrum; (d) marginal autozooids, showing orifice shape; note denticles associated with basal pore chambers; (e) autozooids, with diamond-shaped frontal avicularia and hypertrophied suboral avicularia; (f) ovicelled autozooids. All panels are scanning electron microscopic images of bleached specimens. Scale bars: a = 1.0 mm; b–f = 300 µm.
Figure 27 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 27. (a–c) Robertsonidra argentea (Hincks), NSMT-Te 1149: (a) autozooids near colony margin; (b) autozooids, showing two types of avicularia; (c) ovicelled and non-ovicelled autozooids. (d–f) Robertsonidra porifera (Maplestone), NSMT-Te 1155: (d) autozooids near colony margin, one showing more-common large avicularium; (e) autozooids, one showing uncommon smaller avicularium; (f) ovicelled and non-ovicelled autozooids. All panels are scanning electron microscopic images of bleached specimens. Scale bars = 300 µm.
Figure 1 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 1. Partial map of Japan (lower right) showing the location of Okinawa (upper right), with the study area enlarged (left); black circles indicates sampling sites (SES, old breakwater near Sesoko Station; REEF, reef-fringe site; MIN, breakwater on Minna Island); black square indicates the Sesoko Station, Tropical Biosphere Research Centre, University of the Ryukyus; dark grey shading indicates land; light grey shading indicates areas of coral reef flat.
Figure 20 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 20. (a) Calyptotheca reniformis Tilbrook, 2006, NSMT-Te 1125, ovicelled and several nonovicelled autozooids. (b–d) Calyptotheca sesokoensis sp. nov., NSMT-Te 1128 (holotype): (b) autozooids at colony margin; (c) autozooids, one with rare lateral-oral avicularium; (d) ovicelled and nonovicelled autozooids. All panels are scanning electron microscopic images of bleached specimens. Scale bars = 300 µm.
Figure 6 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 6. (a–d) Corbulella extenuata Dick, Tilbrook, and Mawatari, NSMT-Te 1064: (a) autozooids; (b) oblique view of colony margin showing interzooidal connections and presumed vestigial ooecium at early stage of formation (far top right); (c) ancestrula and periancestrular zooids; (d) same ancestrula (asterisk) as in panel (c) after bleaching, with daughter zooids lost from left side. (e, f) Cranosina coronata (Hincks), NSMT-Te 1065: (e) autozooids (the central three showing regenerative, intramurally budded cystids); (f) autozooids at colony margin (central zooid with intramurally budded cystid). Panels are scanning electron microscopic images of dried (a, c) or bleached (b, d–f) specimens. Scale bars: a = 250 µm; b–d = 300 µm; e, f = 400 µm.
Figure 19 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 19. (a, b) Smittina nitidissima (Hincks), NSMT-Te 1119: (a) autozooids at colony margin; (b) ovicelled autozooids, with 0–2 lateral oral avicularia. (c, d) Smittoidea pacifica Soule and Soule, NSMT-Te 1120: (c) zooids at colony margin; (d) ovicelled and non-ovicelled autozooids. All panels are scanning electron microscopic images of bleached specimens. Scale bars = 300 µm.
Figure 10 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 10. (a) Vasignyella otophora (Kirkpatrick), NSMT-Te 1079: four autozooids from branched, erect colony. (b–h) Hippothoa petrophila sp. nov.: (b) NSMT-Te 1082 (paratype), part of uniserial colony, with two zooidal dilatations, or 'zooids' (arrowheads),linked by long caudal portion, or 'stolon'; (c) NHMUK 2016.5.13.18 (paratype), part of anastomosed uniserial colony; (d) NSMT-Te 1083 (paratype), autozooid with paired proximolateral zooeciules; (e) NSMT-Te 1082 (paratype), autozooidal orifice; (f) photomicrograph of dried specimen showing autozooid (az) that has budded an ovicelled female zooid (fz) from the lateral margin; (g) photomicrographs of the basal side of zooids, showing lateral (arrowheads) and distal (arrow) interzooidal connections; (h) NSMT-Te 1082, presumed ancestrula (a) that has given rise to a single daughter zooid (dz), with a non-connected zooid at lower right. Panels (f) and (g) are photomicrographs; all other panels are scanning electron microscopic images; the specimens in panels (c) to (e) were lightly bleached. Scale bars:a–c = 500 µm; d, h = 150 µm; e = 50 µm; f = 25 µm; g = 10 µm.
Figure 13 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 13. Celleporaria desperabilis Ryland and Hayward, NSMT-Te 1090: (a) young autozooids near colony margin; (b) young autozooids near colony margin, in frontodistal view; (c) primary orifice near colony margin; (d) autozooids, showing suboral avicularium adjacent to sinus; circular interzooidal openings indicated by arrowheads; (e) autozooid with pair of tiny avicularia lateral to orifice, and irregular interzooidal opening (arrowhead); (f) ovicells that appear to be aborted or incompletely developed, bounded by thickened rim distal to orifice. All panels are scanning electron microscopic images of the specimen after bleaching. Scale bars: a = 500 µm; b = 200 µm; c, e = 100 µm; d, f = 250 µm.
Figure 15 in Rocky-intertidal cheilostome bryozoans from the vicinity of the Sesoko Biological Station, west-central Okinawa, Japan
Figure 15. Parasmittina serrula Soule and Soule, (a, b) NSMT-Te 1099, (c, d) NSMT-Te 1100: (a) orifices, showing lyrula and condyles; (b), ovicelled autozooids, with small suboral avicularia; (c) ovicelled autozooids, with larger suboral avicularia; (d) ancestrula and first daughter zooid. All panels are scanning electron microscopic images of bleached specimens. Scale bars: a = 100 µm; b–d = 300 µm.
Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal
<p>While the utility of environmental DNA (eDNA) metabarcoding surveys for biodiversity monitoring continues to be demonstrated, the spatial and temporal variability of eDNA, and thus the limits of the differentiability of an eDNA signal, remains under-characterized. In this study, we collected eDNA samples from distinct micro-habitats (~40 m apart) in a rocky intertidal ecosystem over their exposure period in a tidal cycle. During this period, the micro-habitats transitioned from being interconnected, to physically isolated, to interconnected again. Using a well-established eukaryotic (cytochrome oxidase subunit I) metabarcoding assay, we detected 415 species across 28 phyla. Across a variety of univariate and multivariate analyses, using exclusively taxonomically assigned data as well as all detected amplicon sequence variants (ASVs), we identified unique eDNA signals from the different micro-habitats sampled. This difference paralleled expected ecological gradients and increased as the sites became more physically disconnected. Our results demonstrate that eDNA biomonitoring can differentiate micro-habitats in the rocky intertidal only 40 m apart, that these differences reflect known ecology in the area, and that physical connectivity informs the degree of differentiation possible. These findings showcase the potential power of eDNA biomonitoring to increase the spatial and temporal resolution of marine biodiversity data, aiding research, conservation, and management efforts.</p>
Stability of rocky intertidal communities in response to species removal varies across spatial scales
<p>Improving our understanding of stability across spatial scales is crucial in the current scenario of biodiversity loss. Still, most empirical studies of stability target small scales. Here we experimentally removed the local space-dominant species (macroalgae, barnacles, or mussels) at eight sites spanning more than 1000 km of coastline in north- and south-central Chile, and quantified the relationship between area (the number of aggregated sites) and stability in aggregate community variables (total cover) and taxonomic composition. Resistance, recovery, and invariability increased nonlinearly with area in both functional and compositional domains. Yet, the functioning of larger areas achieved a better, albeit still incomplete, recovery than composition. Compared with controls, smaller disturbed areas tended to overcompensate in terms of total cover. These effects were related to enhanced available space for recruitment (resulting from the removal of the dominant species), and to increasing beta diversity and decaying community-level spatial synchrony (resulting from increasing area). This study provides experimental evidence for the pivotal role of spatial scale in the ability of ecosystems to resist and recover from chronic disturbances. This knowledge can inform further ecosystem restoration and conservation policies.</p>
Fig. 2 in Niche Sharing In Intertidal Mollusks And Decapods In Rocky Shore Of Easter Island
Fig. 2. Probabilistic distribution model for Planes minutus (Linnaeus, 1758) and Leptograpsus variegatus (Fabricius, 1793), Nerita morio (G. B. Sowerby I., 1833) and Nodilittorina pyramidalis pascua Rosewater, 1970 for the studied site, Tahai beach on Easter Island, a rocky shore, sampled in June 2010.
Рис. 15. ПляЖи и пляЖевые танатоценоЗы б. Теляковского (июнь 2015 г.): А – северная часть бухты: пляЖ и валунно-глыбовая литораль; В – срединная часть бухты; С – массовые выбросы устриц (Crassostrea gigas), мидий (Crenomytilus grayanus) и модиолусов (Modiolus kurilensis) в северной части бухты; D – выбросы спиЗулы (Spisula sachalinensis) в срединной части бухты. Fig. 15. Beaches and beach thanatocoenoses of Telyakovskogo Bay (June 2015): A – northern part of the bay: a beach and rocky intertidal zone; B – middle part of the bay; C – abundant strandings of oysters (Crassostrea gigas), mussels (Crenomytilus grayanus and Modiolus kurilensis) in the northern part; D – strandings of Spisula sachalinensis in the middle part. in Mollusks from the shell-midden of the Telyakovskogo 2 site in southern Primorye (Yankovskaya culture), their paleoecology and role in paleoeconomy
Рис. 15. ПляЖи и пляЖевые танатоценоЗы б. Теляковского (июнь 2015 г.): А – северная часть бухты: пляЖ и валунно-глыбовая литораль; В – срединная часть бухты; С – массовые выбросы устриц (Crassostrea gigas), мидий (Crenomytilus grayanus) и модиолусов (Modiolus kurilensis) в северной части бухты; D – выбросы спиЗулы (Spisula sachalinensis) в срединной части бухты. Fig. 15. Beaches and beach thanatocoenoses of Telyakovskogo Bay (June 2015): A – northern part of the bay: a beach and rocky intertidal zone; B – middle part of the bay; C – abundant strandings of oysters (Crassostrea gigas), mussels (Crenomytilus grayanus and Modiolus kurilensis) in the northern part; D – strandings of Spisula sachalinensis in the middle part.
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